Alignments for a candidate for acs in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Acidithiobacillus ferrooxidans ATCC 23270

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_012536874.1 AFE_RS09120 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000021485.1:WP_012536874.1
          Length = 655

 Score =  749 bits (1935), Expect = 0.0
 Identities = 372/656 (56%), Positives = 471/656 (71%), Gaps = 9/656 (1%)

Query: 2   SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61
           ++I+S + E R F  P  FASQA + + E +  L  +A  D +GFW   AR+ L W  PF
Sbjct: 3   TSIDSALSETRSFPVPAHFASQANMDA-ETFARLNRQATEDPDGFWGDLARQHLDWDVPF 61

Query: 62  TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121
            +VL+   APFY+WF  G+LN +YNC+DR+L+     K A+++E +DGSV  VTY +LH 
Sbjct: 62  QRVLEVDQAPFYRWFGGGQLNVAYNCVDRHLRGATRHKAALIWEGEDGSVRTVTYAQLHR 121

Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181
           ++  FAN LK  G++KGDRV IYMPM  E ++AM ACAR+GA H+VVFGGFSA++L++RL
Sbjct: 122 EMSLFANALKHQGVQKGDRVAIYMPMVPEAIIAMLACARIGAIHTVVFGGFSAEALKDRL 181

Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241
            D  A  LITAD   R GK +PLK  AD AL      +VR+VIV RRTG  +   EGRD 
Sbjct: 182 EDTDAKVLITADGAWRAGKMVPLKRHADQALLREHEHSVRHVIVLRRTGADIDMQEGRDI 241

Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301
           W ED  A     C A  + AE  LF+LYTSGSTGKPKGV HS+ GYLLW ++T +W FDI
Sbjct: 242 WWEDAVADVNADCPALSMQAEDTLFILYTSGSTGKPKGVFHSSAGYLLWTMLTTRWVFDI 301

Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361
           KP+D++WCTADIGW+TGH+Y+ YGPLA GAT  ++EG P +P   RFW MIARH +SI Y
Sbjct: 302 KPEDVYWCTADIGWITGHSYVVYGPLANGATVFLYEGAPMHPQPDRFWKMIARHGISILY 361

Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421
           TAPTA+R+ +K  +      P+++DLSSLRLLG+VGEP+NPEAWMWYYK IG  RCP+ D
Sbjct: 362 TAPTAVRAFMKMGDE----WPQRHDLSSLRLLGSVGEPMNPEAWMWYYKQIGGGRCPVAD 417

Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGN-GGILVVKRPW 480
           T+WQTETGGHMI PLPG T   PGSC LPLPGI A IV++ G  +   N GG LV+ RPW
Sbjct: 418 TWWQTETGGHMIAPLPGVTANRPGSCALPLPGISARIVNDQGAPITAPNAGGYLVIDRPW 477

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P M+R +WG+PER+ +SY+      + Y+AGD + RD D GYF +MGRIDDVLNVSGHR+
Sbjct: 478 PGMLRGVWGNPERYVESYW-ARFDNRYYIAGDSARRDAD-GYFWVMGRIDDVLNVSGHRL 535

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GT E+ESALV++P V+EAA+VG P ++ GEAICAFVVLK     G++  ++   LR  V 
Sbjct: 536 GTAEVESALVAHPAVSEAAIVGIPHEIKGEAICAFVVLKHQH-QGDDRDELGAALRAQVT 594

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
           + IG IA+P DIRF D LPKTRSGKIMRRLLRS+A+GEE+TQD STLE+   L+ L
Sbjct: 595 ELIGAIARPDDIRFTDALPKTRSGKIMRRLLRSIARGEEVTQDMSTLEDEGTLQNL 650


Lambda     K      H
   0.319    0.136    0.422 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1402
Number of extensions: 83
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 660
Length of database: 655
Length adjustment: 38
Effective length of query: 622
Effective length of database: 617
Effective search space:   383774
Effective search space used:   383774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_012536874.1 AFE_RS09120 (acetate--CoA ligase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.14326.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-301  987.2   0.0   1.7e-301  987.0   0.0    1.0  1  lcl|NCBI__GCF_000021485.1:WP_012536874.1  AFE_RS09120 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021485.1:WP_012536874.1  AFE_RS09120 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  987.0   0.0  1.7e-301  1.7e-301       3     626 ..      28     650 ..      26     653 .. 0.98

  Alignments for each domain:
  == domain 1  score: 987.0 bits;  conditional E-value: 1.7e-301
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 
                                               ++e++++l ++a+edp+ fw++la+++l+w+ pf++vl+ +++p+++Wf +g+lnv+yncvdrh++  +
  lcl|NCBI__GCF_000021485.1:WP_012536874.1  28 DAETFARLNRQATEDPDGFWGDLARQHLDWDVPFQRVLEVDQAPFYRWFGGGQLNVAYNCVDRHLRGaT 96 
                                               5688999***********************************************************989 PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                               ++k+a+iweg++ +  +r++tYa+l+re++ +an+lk++Gv+kgdrvaiY+pm+pea+iamlacaRiGa
  lcl|NCBI__GCF_000021485.1:WP_012536874.1  97 RHKAALIWEGEDGS--VRTVTYAQLHREMSLFANALKHQGVQKGDRVAIYMPMVPEAIIAMLACARIGA 163
                                               9**********664..8**************************************************** PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgee 207
                                               +h+vvf+Gfsaeal++R++d++ak++itad+++R gk+++lk+ +d+al +++e sv++v+v++rtg++
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 164 IHTVVFGGFSAEALKDRLEDTDAKVLITADGAWRAGKMVPLKRHADQALLREHEhSVRHVIVLRRTGAD 232
                                               ************************************************9887777************** PP

                                 TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
                                               +  ++egrD+wwe++v++ ++a+c++ ++++ed lfiLYtsGstGkPkGv h+++Gyll+++lt+++vf
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 233 ID-MQEGRDIWWEDAVAD-VNADCPALSMQAEDTLFILYTSGSTGKPKGVFHSSAGYLLWTMLTTRWVF 299
                                               76.**************7.************************************************** PP

                                 TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
                                               dik+ed++wCtaD+GW+tGhsY+vygPLanGat +l+eg+p +p+++rfw++i +++++i+YtaPta+R
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 300 DIKPEDVYWCTADIGWITGHSYVVYGPLANGATVFLYEGAPMHPQPDRFWKMIARHGISILYTAPTAVR 368
                                               ********************************************************************* PP

                                 TIGR02188 346 almklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvat 414
                                               a+mk+g+e++++hdlsslr+lgsvGep+npeaw+Wyy+++G ++cp++dtwWqtetGg++i+plpg +t
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 369 AFMKMGDEWPQRHDLSSLRLLGSVGEPMNPEAWMWYYKQIGGGRCPVADTWWQTETGGHMIAPLPG-VT 436
                                               ******************************************************************.5* PP

                                 TIGR02188 415 elkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyf 482
                                               + +pgs++lPl+Gi+a++v+++g ++++ + gg+Lvi++pwP+mlr+++g++er+ve+Y+ ++++ +y+
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 437 ANRPGSCALPLPGISARIVNDQGAPITAPNAGGYLVIDRPWPGMLRGVWGNPERYVESYWARFDNrYYI 505
                                               ***************************77778*******************************987999 PP

                                 TIGR02188 483 tGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                               +GD+arrd+dGy+w++GR+Ddv+nvsGhrlgtae+esalv+h+av+eaa+vg+p+eikgeai+afvvlk
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 506 AGDSARRDADGYFWVMGRIDDVLNVSGHRLGTAEVESALVAHPAVSEAAIVGIPHEIKGEAICAFVVLK 574
                                               ********************************************************************* PP

                                 TIGR02188 552 egveedee.elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstled 619
                                               ++++ d++ el + l+++v++ ig+ia+pd+i+++++lPktRsGkimRRllr+ia+gee+++d+stled
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 575 HQHQGDDRdELGAALRAQVTELIGAIARPDDIRFTDALPKTRSGKIMRRLLRSIARGEEVTQDMSTLED 643
                                               9999776559*********************************************************** PP

                                 TIGR02188 620 psvveel 626
                                               +  +++l
  lcl|NCBI__GCF_000021485.1:WP_012536874.1 644 EGTLQNL 650
                                               *999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (655 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.61
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources